LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 20

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
lattice		fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region		box block 0 $x 0 $y 0 $z
region		box block 0 10 0 $y 0 $z
region		box block 0 10 0 10 0 $z
region		box block 0 10 0 10 0 20
create_box	1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
  2 by 1 by 4 MPI processor grid
create_atoms	1 box
Created 8000 atoms
mass		1 1.0

velocity	all create $t 87287
velocity	all create 1.35 87287

pair_style	lj/cut ${rc}
pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# 1st equilibration run

fix		1 all nvt temp $t $t 0.5
fix		1 all nvt temp 1.35 $t 0.5
fix		1 all nvt temp 1.35 1.35 0.5
thermo		100
run		1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
Loop time of 0.875524 on 8 procs for 1000 steps with 8000 atoms

Performance: 493418.774 tau/day, 1142.173 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48279    | 0.49681    | 0.51174    |   1.2 | 56.74
Neigh   | 0.22868    | 0.23169    | 0.23454    |   0.4 | 26.46
Comm    | 0.084792   | 0.098391   | 0.11603    |   3.4 | 11.24
Output  | 0.00027204 | 0.00027871 | 0.00031137 |   0.1 |  0.03
Modify  | 0.027863   | 0.032316   | 0.039397   |   2.3 |  3.69
Other   |            | 0.01605    |            |       |  1.83

Nlocal:    1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost:    2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs:    27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1

Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0

velocity	all scale $t
velocity	all scale 1.35

unfix		1

# 2nd equilibration run

compute		ke all ke/atom
variable	temp atom c_ke/1.5

fix		1 all nve

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.mp

fix		3 all thermal/conductivity 10 z 20

variable        tdiff equal f_2[11][3]-f_2[1][3]
thermo_style	custom step temp epair etotal f_3 v_tdiff

thermo		1000
run		20000
Memory usage per processor = 2.8078 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff 
    1000         1.35   -3.7100044   -1.6852575            0            0 
    2000    1.3572899   -3.7210084   -1.6853282    873.12373   0.26058005 
    3000     1.359979   -3.7268343   -1.6871208    1750.6998   0.40845169 
    4000    1.3677509   -3.7394553   -1.6880853    2565.8064   0.63828485 
    5000    1.3742987    -3.750287   -1.6890966    3373.2897   0.70173279 
    6000    1.3950535   -3.7827674   -1.6904487    4162.6672   0.83210131 
    7000    1.3843852   -3.7679238   -1.6916056    4947.5882   0.92719731 
    8000     1.396125   -3.7861373   -1.6922116    5703.4508   0.92426948 
    9000    1.4135104    -3.812624   -1.6926234    6465.5676    1.0412501 
   10000    1.4092351   -3.8065359   -1.6929474    7242.2986    1.0772505 
   11000    1.3966916   -3.7874302   -1.6926547    8007.3229     1.056805 
   12000    1.4111272   -3.8089829   -1.6925567    8750.8648     1.097621 
   13000    1.4091888   -3.8074873   -1.6939684    9514.7196    1.0734167 
   14000    1.4132159   -3.8134636   -1.6939046    10284.269    1.1643391 
   15000    1.3991348   -3.7928819    -1.694442    11051.851    1.0716016 
   16000    1.4055537   -3.8013252   -1.6932583    11836.812    1.1506479 
   17000    1.4127928   -3.8141054   -1.6951811    12626.124    1.1301728 
   18000    1.4118868   -3.8119733   -1.6944077    13391.631    1.1521394 
   19000    1.4209268    -3.826811   -1.6956872    14180.009    1.0929393 
   20000    1.4093812   -3.8083875   -1.6945801    14969.574    1.2113183 
   21000    1.4202317   -3.8255696   -1.6954884    15735.893     1.161082 
Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms

Performance: 409982.223 tau/day, 949.033 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.4932     | 10.005     | 12.426     |  70.1 | 47.48
Neigh   | 4.0592     | 5.0894     | 6.0544     |  41.7 | 24.15
Comm    | 1.7793     | 5.0312     | 8.5027     | 134.6 | 23.87
Output  | 0.00058484 | 0.00060964 | 0.0007031  |   0.1 |  0.00
Modify  | 0.39735    | 0.4211     | 0.43467    |   2.3 |  2.00
Other   |            | 0.5269     |            |       |  2.50

Nlocal:    1000 ave 1188 max 806 min
Histogram: 2 1 1 0 0 0 0 0 2 2
Nghost:    2300.5 ave 2645 max 1963 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs:    27897 ave 37064 max 18367 min
Histogram: 2 2 0 0 0 0 0 0 0 4

Total # of neighbors = 223176
Ave neighs/atom = 27.897
Neighbor list builds = 3537
Dangerous builds = 0

# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation

fix		3 all thermal/conductivity 10 z 20

fix             ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style	custom step temp epair etotal f_3 v_tdiff f_ave

run		20000
Memory usage per processor = 3.05853 Mbytes
Step Temp E_pair TotEng f_3 v_tdiff f_ave 
   21000    1.4202317   -3.8255696   -1.6954884            0     1.161082     1.161082 
   22000    1.4090517    -3.808543   -1.6952296    745.83128    1.1780376    1.1695598 
   23000    1.4261394   -3.8350237    -1.696082    1516.9526    1.1393504      1.15949 
   24000    1.4103907   -3.8098769   -1.6945553    2290.0213    1.1962529    1.1686807 
   25000    1.4205929   -3.8266444   -1.6960213    3028.2748    1.1355183    1.1620482 
   26000    1.4148587   -3.8168728     -1.69485    3788.0858    1.1902606    1.1667503 
   27000    1.4226648   -3.8297832   -1.6960528    4580.4932    1.2378446    1.1769066 
   28000    1.4167854   -3.8205958   -1.6956834    5328.2357    1.2038835    1.1802787 
   29000    1.4208636   -3.8267081   -1.6956791     6077.036    1.1970863    1.1821462 
   30000     1.420575   -3.8256917   -1.6950955    6840.5407    1.1884497    1.1827766 
   31000    1.4233235   -3.8318045   -1.6970861    7576.9859    1.2088723    1.1851489 
   32000     1.418912   -3.8229407   -1.6948388    8319.9854    1.1604002    1.1830865 
   33000    1.4161289   -3.8211375   -1.6972096    9097.8598    1.1381183    1.1796274 
   34000    1.3982574   -3.7915345   -1.6944106    9819.5817    1.1809721    1.1797235 
   35000    1.4211314   -3.8267235   -1.6952929    10604.381     1.157812    1.1782627 
   36000    1.4181668   -3.8217718   -1.6947876    11332.942    1.1843186    1.1786412 
   37000    1.4092823   -3.8094817   -1.6958226     12068.55    1.1043391    1.1742705 
   38000    1.4220481   -3.8278441   -1.6950386    12815.406    1.1996255    1.1756791 
   39000    1.4146432   -3.8175526   -1.6958531    13565.714     1.149226    1.1742868 
   40000    1.4088356   -3.8079173    -1.694928    14309.801    1.1710565    1.1741253 
   41000    1.4058693   -3.8043119   -1.6957716    15067.894    1.1839862    1.1745949 
Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms

Performance: 391962.361 tau/day, 907.320 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.8314     | 10.063     | 12.978     |  88.0 | 45.65
Neigh   | 3.8802     | 5.2398     | 6.5269     |  52.7 | 23.77
Comm    | 1.828      | 5.8112     | 10.14      | 160.2 | 26.36
Output  | 0.00050211 | 0.00052819 | 0.00060391 |   0.1 |  0.00
Modify  | 0.39313    | 0.41984    | 0.4453     |   3.3 |  1.90
Other   |            | 0.5084     |            |       |  2.31

Nlocal:    1000 ave 1188 max 810 min
Histogram: 2 1 1 0 0 0 0 1 1 2
Nghost:    2304.5 ave 2648 max 1970 min
Histogram: 3 1 0 0 0 0 0 0 1 3
Neighs:    27885.2 ave 36431 max 18556 min
Histogram: 2 2 0 0 0 0 0 0 1 3

Total # of neighbors = 223082
Ave neighs/atom = 27.8852
Neighbor list builds = 3626
Dangerous builds = 0
Total wall time: 0:00:44
